Manipulation of nucleic acids has been used for decades in numerous applications in a variety of fields of biological science. One of the fundamental processes that has enabled the diverse utility of nucleic acid manipulation is the ability to cleave nucleic acid. Typically, cleavage of DNA/cDNA is mediated by restriction endonucleases, which are a class of enzymes that recognize short (6-15 bp) specific sequences of DNA/cDNA called restriction sites, which must be present in the DNA/cDNA being cleaved. Cleaving DNA/cDNA at a sequence-specific location typically requires that there be a commercially available restriction endonuclease that is specific for the sequence in the desired cleavage location and that this enzyme naturally cleaves in the exact base-pair location within the recognition sequence that is desired. Because restriction endonucleases cleave all compatible recognition sites present, their utility is limited if the recognition site is present in locations where cleavage is not desired. Thus, the usefulness of restriction enzyme mediated cleavage is limited in emerging technologies that are high-throughput, have complex template, or have regions where the exact template sequence is unknown. It has been a challenge to develop a robust, flexible and cost-effective method for highly specific targeted cleavage of nucleic acids into fragments that are optimal and agnostic for downstream applications.